4DAV | pdb_00004dav

The structure of Pyrococcus Furiosus SfsA in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb4DAV/pdb
• NAKB: 4DAV

• Classification: HYDROLASE/DNA
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-13 Released: 2014-10-01 
• Deposition Author(s): Baker, P.J., Allen, F.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.298 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

The structure of SfsA and its DNA complex; A DNA/RNA nuclease with a novel domain combination

Allen, F.L., Akerboom, J., Bliss, S.J., Blombach, F., Sedelnikova, S.E., van der Oost, J., Baker, P.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.67 kDa 
• Atom Count: 4,335 
• Modeled Residue Count: 486 
• Deposited Residue Count: 486 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar fermentation stimulation protein homolog	A, B	231	Pyrococcus furiosus DSM 3638	Mutation(s): 1  Gene Names: sfsA, PF1198
UniProt
Find proteins for Q8U1K8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U1K8  Go to UniProtKB:  Q8U1K8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*TP*GP*TP*CP*TP*CP*GP*CP*T)-3'	C [auth X], D	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.298 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.7	α = 90
b = 42.69	β = 104.92
c = 88.9	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Baker, P.J., Allen, F.L.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description